This is the old Macintosh issue that got fixed, then rebroken and never re-fixed.
Yes, the X works (but why would anyone think that exits the application?).
But Quit from the menu, shortcut key, dock menu, etc. do not work.

I often help out colleagues, friends, e.g. people that have "apps" running and often I find tons of idle apps not turned off in the background - because it's usually not something one thinks about having to do. Most press menu to get out and leave it running - draining battery in the background.

I close my apps with "sudo pkill" cause I'm a Linux rockin command line pro!

Course I'm pretty sure minion doesn't run on Linux but I haven't tried it either.

If you grab the app directory from the exe or the java directory from the dmg and run Minion-jfx.jar with the lib folder in a subdirectory it should run from Linux. It requires Java8 if you run it that way.

Re-opened the bug ticket for this, your right it was fixed for awhile (back when Minion was Java7) and I'm guessing in Java8 things changed again because the fix was kind of a hack. Also a lot of areas were re-worked/re-written and it might have been reintroduced then.